Do not disclose "methodologies" if you fear clones.
If it so trivial that even children could reimplement it,
then your methodologies worth nothing.

Actually, being simple to implement is exactly what makes them brilliant. If it is something simple to implement, but still novel, then it is even more valuable than if it is very complex. It can be simple to implement without being obvious.

I am not saying that software patents are good, or that our current system is even close to functional. I am saying that these are the things we need to consider as we fix it.